Nations hosts Egypt ensured they emerged from Group A with a perfect record despite a stern examination by Uganda.
Liverpool striker Salah's free-kick and a second goal from Aston Villa midfielder Ahmed Elmohamady before the break secured a 2-0 win.
But the scoreline flattered them on a night when Sebastien Desabre's side, who finished second in the group with four points and take their place in the last-16, more than gave as good as they got in Cairo.
Egypt keeper Mohamed El-Shenawy had made a number of good saves before Salah curled a left-foot free-kick over the wall and past keeper Denis Onyango in the 36th minute.
Skipper Elmohamady smashed home a second in first-half stoppage time to clinch a third successive victory for Egypt, all without conceding a goal.
Salah almost made it 3-0 early in the second half, only to be denied Onyango, who is a doubt for the knockout phase after being stretchered off with 18 minutes remaining.
